The nanomaterials-filled thermoset/thermoplastic ternary nanocomposites exhibit important potential to achieve both toughening and stiffening effect for thermosetting resin. However, the targeted growth in fracture toughness and the synergistic toughening mechanism of thermoplastic resin and nanomaterials has not been attained due to the complex immiscible ternary system. In this work, thermoplastic resin polyetherketone-cardo (PEK-C) and carbon nanotubes (CNTs) were synergistically incorporated in thermosetting epoxy (EP) resin. The structure-property correlation was explored via the investigation of mechanical performance and microstructure. The results showed that the change of fracture toughness was not linearly related to the PEK-C content, while closely related to the dualphase structure formed by EP and PEK-C. After introducing CNTs, the CNTs were selectively located in the continuous phase of EP, which increased the viscosity of the located region and hindered the coarsening and interconnecting of the dispersed phase of PEK-C, weakening the toughening effect of dualphase structure.